From nobody Sat Sep 14 13:23:34 2024 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4X5X1f5T0Lz5WKPV; Sat, 14 Sep 2024 13:23:34 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4X5X1f2R2gz4Sxt; Sat, 14 Sep 2024 13:23:34 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1726320214; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=b2Jo4lYqj6wIqpio5pgC82Icoebg8NW8rS3QnlaarBk=; b=HXOcM0f81O740drqmzAitIW/5xJgK6g4gF27MGWDQqDcGI7mljXtjlnCuQS/tXTYRf5WOq Vpg0hLYxY61ssZxKQJzTpbU2cuTIPusiwTMkI/hA7fsEFkgIiuT9fO5bJoTx2DlCooLnAD is75jVLVkEV3UVdEnIXsXg5Ybwkr1pI6Q3pDLWoJ2541Kyi5pUs81g4R3tC4q/yYndBGBE 3L2jfvVZ8iyg+0Xs099Pf0QyId9ts0h57ujZyhNK0YrwsCT2oU0Xa0DpCSMLAOciOm2AYK f22CyLpm+IJLcAh1limy5BbPuL44L/0e13uWkBzZPBiPPUR1k72MjmstlCwkYw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1726320214; a=rsa-sha256; cv=none; b=UF1ouSoJwE0zkvFb8MP66A89qZ6T6bpG84ZSubv4fSTHo3OrZxwmAJ9NcqNiB2C7XsmKHU bQSSEREFo6iLYj297hph40/K2/vN29ZGcl/V76sV/xuEzWOoKi3pqBVDijT4o7NkA1dB6C F677CML2LqX/ceOJfxHB9K1n1XS8j+RBkZo3KqcAhu2gCjZeat454vbT4JUKH7QiQtj+Go 8ubwPOdIi3fHHM6uMsp3bwpvgS4lyZhYfv252nkW8QT03CLntty6bz3XxtxK3oHpo/JsYB yfPdjNLAtvpvpDUzl86xDhbCQf9lHEP1UlNBMunWiehYUms6yxbId3dTIB5azA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1726320214; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=b2Jo4lYqj6wIqpio5pgC82Icoebg8NW8rS3QnlaarBk=; b=AMXlOKpImB640HVTN3B4NghOopA+K3cxV3jYtTejLhApq1ZRomXOHxeudUnPTAidr2JyPL TnrOsGVSPn9alJWjsYJJVU/HMuJAhIwcwVDtK8jL2Ms8fOo9hN/TXrB2tLNlRrTrPwMkp4 mcJU5WkjmGQMtaWUEEgUqzlDhv9Cu6hjNrJcFdJFCW1LYM1UFtM0G2av4WEJm1IYvcFIqx qxkYqtQRosqbA+HO23Xk7zwzSS0DQbdMdwqDC9/5uBoKl8RYUnFe+zJ/WSyGFWHN3EbSEJ OqkrOaJd12fk0nIJ24HG6qEZZhw/3P2Zj2ky/nG2oHyxdlxq1WwvybC1G3EAaA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4X5X1f1mygzTKm; Sat, 14 Sep 2024 13:23:34 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 48EDNYA2025999; Sat, 14 Sep 2024 13:23:34 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 48EDNYgR025996; Sat, 14 Sep 2024 13:23:34 GMT (envelope-from git) Date: Sat, 14 Sep 2024 13:23:34 GMT Message-Id: <202409141323.48EDNYgR025996@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: fbb86e94a87c - main - biology/py-macs3: Update to 3.0.2 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: fbb86e94a87c238d1214b49f06b0f955e0f517a0 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fbb86e94a87c238d1214b49f06b0f955e0f517a0 commit fbb86e94a87c238d1214b49f06b0f955e0f517a0 Author: Jason W. Bacon AuthorDate: 2024-09-14 13:22:03 +0000 Commit: Jason W. Bacon CommitDate: 2024-09-14 13:23:32 +0000 biology/py-macs3: Update to 3.0.2 Some minor enhancements and improved docs Changes: https://github.com/macs3-project/MACS/releases Reported by: portscout --- biology/py-macs3/Makefile | 9 ++++----- biology/py-macs3/distinfo | 6 +++--- biology/py-macs3/files/patch-pyproject.toml | 6 +++--- biology/py-macs3/files/patch-requirements.txt | 19 +++++++++++-------- biology/py-macs3/files/patch-setup.py | 11 ----------- 5 files changed, 21 insertions(+), 30 deletions(-) diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile index 56f6bdc9c904..2ca2822457a4 100644 --- a/biology/py-macs3/Makefile +++ b/biology/py-macs3/Makefile @@ -1,6 +1,6 @@ PORTNAME= MACS3 DISTVERSIONPREFIX= v -DISTVERSION= 3.0.1 +DISTVERSION= 3.0.2 CATEGORIES= biology python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,15 +14,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE NOT_FOR_ARCHS= i386 NOT_FOR_ARCHS_REASON_i386=Requires _Float16 -BUILD_DEPENDS= ${PY_SETUPTOOLS} \ - ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ ${PYNUMPY} \ simde>0:devel/simde \ ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} + ${PYTHON_PKGNAMEPREFIX}hmmlearn>=0.3.2:math/py-hmmlearn@${PY_FLAVOR} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ bash:shells/bash diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo index b742493c53a1..bacae8bd911a 100644 --- a/biology/py-macs3/distinfo +++ b/biology/py-macs3/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1713397031 -SHA256 (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 8a2f5b2dccfc255ea2fd5e54e0d6aa9c12f5ce83762b17b779ce2546ade860ce -SIZE (macs3-project-MACS-v3.0.1_GH0.tar.gz) = 197400439 +TIMESTAMP = 1725973815 +SHA256 (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 33e877460f1b621ee85c78221b52d1e067b8f5aacdaf4d16bd887485bf636e08 +SIZE (macs3-project-MACS-v3.0.2_GH0.tar.gz) = 197484503 diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml index 15f55a86a701..94a5699aa764 100644 --- a/biology/py-macs3/files/patch-pyproject.toml +++ b/biology/py-macs3/files/patch-pyproject.toml @@ -1,7 +1,7 @@ ---- pyproject.toml.orig 2024-02-23 05:43:44 UTC +--- pyproject.toml.orig 2024-09-07 16:11:35 UTC +++ pyproject.toml @@ -1,3 +1,3 @@ [build-system] --requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.4', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] -+requires=['setuptools>=60.0', 'numpy>=1.24.2', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0', 'scikit-learn>=1.2.1', 'hmmlearn>=0.3'] +-requires=['setuptools>=68.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.12', 'cykhash>=2.0,<3.0', 'Cython>=3.0,<3.1', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2'] ++requires=['setuptools>=63.0', 'numpy>=1.25,<2.0.0', 'scipy>=1.11.1', 'cykhash>=2.0,<3.0', 'Cython>=0.29.37', 'scikit-learn>=1.3', 'hmmlearn>=0.3.2'] diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt index 81c9a1f75f88..ceac91b3141e 100644 --- a/biology/py-macs3/files/patch-requirements.txt +++ b/biology/py-macs3/files/patch-requirements.txt @@ -1,11 +1,14 @@ ---- requirements.txt.orig 2024-02-23 05:43:44 UTC +--- requirements.txt.orig 2024-09-07 16:11:35 UTC +++ requirements.txt -@@ -1,6 +1,6 @@ --Cython~=3.0 -+Cython>=0 - numpy>=1.24.2 --scipy>=1.11.4 +@@ -1,8 +1,8 @@ +-Cython>=3.0,<3.1 ++Cython>=0.29.37 + numpy>=1.25,<2.0.0 +-scipy>=1.12 +scipy>=1.11.1 - scikit-learn>=1.2.1 - hmmlearn>=0.3 + scikit-learn>=1.3 + hmmlearn>=0.3.2 cykhash>=2.0,<3.0 + pytest>=7.0 +-setuptools>=68.0 ++setuptools>=63.0 diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py deleted file mode 100644 index f309f3139736..000000000000 --- a/biology/py-macs3/files/patch-setup.py +++ /dev/null @@ -1,11 +0,0 @@ ---- setup.py.orig 2024-02-24 14:39:02 UTC -+++ setup.py -@@ -70,7 +70,7 @@ def main(): - - if not clang: - try: -- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True) -+ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True) - if gcc_version_check.find("clang") != -1: - clang = True - else: